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- PDB-3sx6: Crystal structure of sulfide:quinone oxidoreductase Cys356Ala var... -

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Basic information

Entry
Database: PDB / ID: 3sx6
TitleCrystal structure of sulfide:quinone oxidoreductase Cys356Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone
ComponentsSulfide-quinone reductase
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys356Ala variant / integral monotopic membrane protein / complex with sulfide and decylubiquinone
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / NAD(P)H dehydrogenase (quinone) activity / aerobic electron transport chain / quinone binding / nucleotide binding / membrane
Similarity search - Function
: / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-DCQ / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7955 Å
AuthorsCherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structure-activity characterization of sulfide:quinone oxidoreductase variants.
Authors: Cherney, M.M. / Zhang, Y. / James, M.N. / Weiner, J.H.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 2.0Mar 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref_seq_dif.details
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6778
Polymers47,7981
Non-polymers1,8797
Water6,143341
1
A: Sulfide-quinone reductase
hetero molecules

A: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,35416
Polymers95,5962
Non-polymers3,75814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8590 Å2
ΔGint-114 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.828, 149.828, 81.513
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-629-

HOH

31A-632-

HOH

41A-671-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase / SQR / Sulfide:quinone oxidoreductase


Mass: 47798.023 Da / Num. of mol.: 1 / Mutation: C356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria)
Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: Escherichia coli (E. coli)
References: UniProt: B7JBP8, bacterial sulfide:quinone reductase
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 347 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 600, 0.1 M bis-tris buffer,0.1 M MgSO4, 0.05% DDM, 2 mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: DCM, Si(111) cryo-cooled first crystal and sagittally bent second
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7955→50 Å / Num. all: 50553 / Num. obs: 46610 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 32.2
Reflection shellResolution: 1.7955→1.86 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.83 / Num. unique all: 3202 / Rsym value: 0.749 / % possible all: 64.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7955→30.14 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2376 5.11 %RANDOM
Rwork0.1788 ---
obs0.1809 46540 91.97 %-
all-50587 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.235 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1212 Å20 Å20 Å2
2---6.1212 Å2-0 Å2
3---12.2423 Å2
Refinement stepCycle: LAST / Resolution: 1.7955→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 125 341 3687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063456
X-RAY DIFFRACTIONf_angle_d1.0784688
X-RAY DIFFRACTIONf_dihedral_angle_d20.5931313
X-RAY DIFFRACTIONf_chiral_restr0.076504
X-RAY DIFFRACTIONf_plane_restr0.008589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7955-1.83220.35181010.32471627X-RAY DIFFRACTION59
1.8322-1.8720.37271140.28641917X-RAY DIFFRACTION69
1.872-1.91560.32761010.24462186X-RAY DIFFRACTION78
1.9156-1.96340.2461140.21392384X-RAY DIFFRACTION85
1.9634-2.01650.23521420.19882505X-RAY DIFFRACTION90
2.0165-2.07580.21491440.1992615X-RAY DIFFRACTION94
2.0758-2.14280.26961470.19112700X-RAY DIFFRACTION97
2.1428-2.21940.27071400.18992748X-RAY DIFFRACTION99
2.2194-2.30820.2371710.19092766X-RAY DIFFRACTION99
2.3082-2.41320.26981440.18792804X-RAY DIFFRACTION100
2.4132-2.54040.27311640.19572803X-RAY DIFFRACTION100
2.5404-2.69950.25051310.20092817X-RAY DIFFRACTION99
2.6995-2.90770.23521440.20582803X-RAY DIFFRACTION99
2.9077-3.20010.24071460.19712825X-RAY DIFFRACTION99
3.2001-3.66240.22541600.16822823X-RAY DIFFRACTION99
3.6624-4.61160.15541700.13472842X-RAY DIFFRACTION98
4.6116-30.1440.18231430.16182999X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54610.6045-0.20411.6119-0.32660.29140.0624-0.1325-0.08570.3068-0.05560.17550.0303-0.1562-0.01150.2346-0.0660.03490.30470.02740.183640.584-26.77612.1828
20.70480.3109-0.28081.1121-0.13830.20510.0976-0.0595-0.04640.0161-0.2009-0.67-0.04790.1390.02610.1998-0.0339-0.04790.21610.0480.385864.4777-17.15866.2074
30.50550.727-0.36551.4912-0.51380.4488-0.05170.1739-0.066-0.20620.0719-0.06120.1874-0.15830.00420.2167-0.0493-0.00330.283-0.00260.165745.5926-25.8538-2.548
40.63490.6005-0.05871.6406-0.43760.3510.0217-0.09110.0962-0.10040.16780.22280.0039-0.3123-0.02970.2475-0.0192-0.0160.31650.03110.251243.4886-10.2781-1.9944
50.73550.6578-0.61061.0252-0.57310.53790.0774-0.07730.25860.38620.01480.2096-0.0837-0.0857-0.07110.32260.00110.08670.3057-0.01330.302642.1319-7.239411.6927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 1:161)
2X-RAY DIFFRACTION2chain A and (resseq 162:232)
3X-RAY DIFFRACTION3chain A and (resseq 233:341)
4X-RAY DIFFRACTION4chain A and (resseq 342:377)
5X-RAY DIFFRACTION5chain A and (resseq 378:410)

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